How to overlay Alpha masked image over finished Video without re-rendering the whole track?
The only way I know is to split the video in two parts (200 frames and the rest), do the changes to the first part, render it, and than join the parts. 
BUT! To join parts without decoding the second one, you must render the first one with exactly the same parameters (codecs and so on). There are different programs for splitting and joining footage without decoding. It's not a problem to find one. But the main problem will be to adjust rendering parameters for the part that will be changed. Otherwise it will be decoded and than it all doesn't make any sense.